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Modern approaches for identification of modified nucleotides in RNA

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Abstract

This review considers approaches for detection of modified monomers in the RNA structure of living organisms. Recently, some data on dynamic alterations in the pool of modifications of the key RNA species that depend on external factors affecting the cells and physiological conditions of the whole organism have been accumulated. The recent studies have presented experimental data on relationship between the mechanisms of formation of modified/minor nucleotides of RNA in mammalian cells and the development of various pathologies. The development of novel methods for detection of chemical modifications of RNA nucleotides in the cells of living organisms and accumulation of knowledge on the contribution of modified monomers to metabolism and functioning of individual RNA species establish the basis for creation of novel diagnostic and therapeutic approaches. This review includes a short description of routine methods for determination of modified nucleotides in RNA and considers in detail modern approaches that enable not only detection but also quantitative assessment of the modification level of various nucleotides in individual RNA species.

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Abbreviations

CMC:

N-cyclohexyl-N′-(2-(4-methyl)morpholinoethyl)carbodiimide tosylate

DMS:

dimethyl sulfate

ds:

double-stranded

HTS:

high-throughput sequencing

I:

inosine

1M7:

1-methyl-7-nitroisatoic anhydride

m5C:

5-methylcytidine

m6A:

N6-methyladenosine

mN:

nucleotide modified at the base

MS:

mass spectrometry

Nm:

nucleotide methylated at the 2′-O-position

NMIA:

N-methylisatoic anhydride

2′-O-Me:

2′-O-methyl group

pre-mRNA:

precursor of mRNA

RNP:

ribonucleoprotein

RT:

reverse transcription

RT-PCR:

reverse transcription followed by polymerase chain reaction

snRNA:

small nuclear RNA

snoRNA:

small nucleolar RNA

ss:

single-stranded

Ψ:

pseudouridine

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Authors and Affiliations

  1. Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia

    J. A. Filippova, D. V. Semenov, E. S. Juravlev, V. A. Richter & G. A. Stepanov

  2. Novosibirsk State University, 630090, Novosibirsk, Russia

    E. S. Juravlev & G. A. Stepanov

  3. Research Institute of Influenza, 197376, St. Petersburg, Russia

    A. B. Komissarov

  4. St. Petersburg University, 199034, St. Petersburg, Russia

    A. B. Komissarov

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  1. J. A. Filippova
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  3. E. S. Juravlev
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  6. G. A. Stepanov
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Original Russian Text © J. A. Filippova, D. V. Semenov, E. S. Juravlev, A. B. Komissarov, V. A. Richter, G. A. Stepanov, 2017, published in Biokhimiya, 2017, Vol. 82, No. 11, pp. 1557–1576.

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Filippova, J.A., Semenov, D.V., Juravlev, E.S. et al. Modern approaches for identification of modified nucleotides in RNA. Biochemistry Moscow 82, 1217–1233 (2017). https://doi.org/10.1134/S0006297917110013

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